/* ------- begin -------------------------- readConvergence.c --- */
void readConvergence(void) {
/* This is a self-contained function to read the convergence matrix,
written by RH. */
const char routineName[] = "readConvergence";
char *atmosID;
int ncid, ncid_mpi, nx, ny;
size_t attr_size;
hid_t plist;
H5T_class_t type_class;
mpi.rh_converged = matrix_int(mpi.nx, mpi.ny);
/* --- Open the inputdata file --- */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fopen(INPUTDATA_FILE, H5F_ACC_RDWR, plist) ) < 0)
HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* Get ncid of the MPI group */
if (( ncid_mpi = H5Gopen(ncid, "mpi", H5P_DEFAULT) ) < 0) HERR(routineName);
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid, "/", "nx", &nx) ) < 0) HERR(routineName);
if (nx != mpi.nx) {
sprintf(messageStr,
"Number of x points mismatch: expected %d, found %d.",
mpi.nx, (int)nx);
Error(WARNING, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid, "/", "ny", &ny) ) < 0) HERR(routineName);
if (ny != mpi.ny) {
sprintf(messageStr,
"Number of y points mismatch: expected %d, found %d.",
mpi.ny, (int)ny);
Error(WARNING, routineName, messageStr);
}
/* --- Read variable --- */
if (( H5LTread_dataset_int(ncid_mpi, CONV_NAME,
mpi.rh_converged[0]) ) < 0) HERR(routineName);
/* --- Close inputdata file --- */
if (( H5Gclose(ncid_mpi) ) < 0) HERR(routineName);
if (( H5Fclose(ncid) ) < 0) HERR(routineName);
return;
}
int_f
nh5ltget_attribute_int_c(hid_t_f *loc_id,
int_f *namelen,
_fcd dsetname,
int_f *attrnamelen,
_fcd attrname,
void *buf)
{
int ret_value = -1;
herr_t ret;
hid_t c_loc_id;
char *c_name = NULL;
char *c_attrname = NULL;
int c_namelen;
int c_attrnamelen;
/*
* convert FORTRAN name to C name
*/
c_namelen = (int)*namelen;
c_name = (char *)HD5f2cstring(dsetname, c_namelen);
if (c_name == NULL)
goto done;
c_attrnamelen = (int)*attrnamelen;
c_attrname = (char *)HD5f2cstring(attrname, c_attrnamelen);
if (c_attrname == NULL)
goto done;
/*
* call H5LTget_attribute_int function.
*/
c_loc_id = (hid_t)*loc_id;
if(sizeof(int_f) == sizeof(int))
ret = H5LTget_attribute_int(c_loc_id,c_name,c_attrname,buf);
else if (sizeof(int_f) == sizeof(long))
ret = H5LTget_attribute_long(c_loc_id,c_name,c_attrname,buf);
else if (sizeof(int_f) == sizeof(long long))
ret = H5LTget_attribute_long_long(c_loc_id,c_name,c_attrname,buf);
else
goto done;
if (ret < 0)
goto done;
ret_value = 0;
done:
if(c_name!=NULL)
free(c_name);
if(c_attrname!=NULL)
free(c_attrname);
return ret_value;
}
// Read integer attribute <attr_name> given by address <path>
char AH5_read_int_attr(hid_t loc_id, const char *path, char *attr, int *rdata)
{
char success = AH5_FALSE;
if (AH5_path_valid(loc_id, path))
if (H5Aexists_by_name(loc_id, path, attr, H5P_DEFAULT) > 0)
if (H5LTget_attribute_int(loc_id, path, attr, rdata) >= 0)
success = AH5_TRUE;
if(!success)
*rdata = 0;
return success;
}
static void
psc_fields_single_read(struct psc_fields *flds, struct mrc_io *io)
{
int ierr;
long h5_file;
mrc_io_get_h5_file(io, &h5_file);
hid_t group = H5Gopen(h5_file, mrc_io_obj_path(io, flds), H5P_DEFAULT); H5_CHK(group);
int ib[3], im[3], nr_comp;
ierr = H5LTget_attribute_int(group, ".", "p", &flds->p); CE;
ierr = H5LTget_attribute_int(group, ".", "ib", ib); CE;
ierr = H5LTget_attribute_int(group, ".", "im", im); CE;
ierr = H5LTget_attribute_int(group, ".", "nr_comp", &nr_comp); CE;
for (int d = 0; d < 3; d++) {
assert(ib[d] == flds->ib[d]);
assert(im[d] == flds->im[d]);
}
assert(nr_comp == flds->nr_comp);
psc_fields_setup(flds);
ierr = H5LTread_dataset_float(group, "fields_single", flds->data); CE;
ierr = H5Gclose(group); CE;
}
int getTimesUsed(PIOTimeline pioTimeline)
{
ERROR_SWITCH_INIT
int times_used = -1;
herr_t get_err;
ERROR_SWITCH_OFF
get_err = H5LTget_attribute_int(pioTimeline.identifier, ".", PIOAttribute_TimesUsed, ×_used);
ERROR_SWITCH_ON
if (get_err < 0) return -1;
return times_used;
}
int pioReadAttributeInteger(PIOObject pioObject,
const char* attr_name, int* attr_value)
{
if (pioHasAttribute(pioObject, attr_name))
{
H5LTget_attribute_int(pioObject.identifier, ".",
attr_name, attr_value);
return 1;
}
else {
return -1;
}
}
//-*****************************************************************************
ArImpl::ArImpl( const std::string &iFileName,
AbcA::ReadArraySampleCachePtr iCache )
: m_fileName( iFileName )
, m_file( -1 )
, m_readArraySampleCache( iCache )
{
// OPEN THE FILE!
htri_t exi = H5Fis_hdf5( m_fileName.c_str() );
ABCA_ASSERT( exi == 1, "Nonexistent File: " << m_fileName );
m_file = H5Fopen( m_fileName.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
ABCA_ASSERT( m_file >= 0,
"Could not open file: " << m_fileName );
// get the version using HDF5 native calls
int version = -INT_MAX;
if (H5Aexists(m_file, "abc_version"))
{
H5LTget_attribute_int(m_file, ".", "abc_version", &version);
}
ABCA_ASSERT(version == ALEMBIC_HDF5_FILE_VERSION,
"Unsupported file version detected.");
// if it isn't there, it's pre 1.0
int fileVersion = 9999;
if (H5Aexists( m_file, "abc_release_version" ))
{
H5LTget_attribute_int( m_file, ".", "abc_release_version",
&fileVersion);
}
m_archiveVersion = fileVersion;
// Read the top object
m_top = new TopOrImpl( *this, m_file );
ReadTimeSamples( m_file, m_timeSamples );
}
//-*****************************************************************************
HDF5HierarchyReader::HDF5HierarchyReader( hid_t iFile,
HDF5Hierarchy& iH5H,
const bool iCacheHierarchy )
: m_H5H( iH5H )
{
int enabled( 0 );
if (iCacheHierarchy && H5Aexists( iFile, "abc_ref_hierarchy" ))
{
H5LTget_attribute_int( iFile, ".", "abc_ref_hierarchy", &enabled );
}
m_H5H.clear();
m_H5H.setEnabled( enabled != 0 );
if( enabled )
{
readHierarchy( iFile );
}
}
/* ------- begin -------------------------- readMolPops_p.c -- */
void readMolPops(Molecule *molecule) {
/* --- Read populations from file.
Note: readPopulations only reads the true populations and not
the LTE populations.
-- -------------- */
const char routineName[] = "readMolPops";
char group_name[ARR_STRLEN], *atmosID;
int nz, nlevel;
H5T_class_t type_class;
size_t attr_size;
hsize_t offset[] = {0, 0, 0, 0};
hsize_t count[] = {1, 1, 1, 1};
hsize_t dims[4];
hid_t ncid, file_dspace, mem_dspace, pop_var;
/* --- Open molecule group --- */
sprintf(group_name, "molecule_%s", molecule->ID);
if (( ncid = H5Gopen(io.aux_ncid, group_name, H5P_DEFAULT) ) < 0)
HERR(routineName);
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(io.aux_ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(io.aux_ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid, ".", "nlevel_vibr", &nlevel) ) < 0)
HERR(routineName);
if (nlevel != molecule->Nv) {
sprintf(messageStr,
"Number of levels mismatch: expected %d, found %d.",
molecule->Nv, (int)nlevel);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(io.aux_ncid, ".", "nz", &nz) ) < 0)
HERR(routineName);
if (nz < atmos.Nspace) {
sprintf(messageStr,
"Number of depth points mismatch: expected %ld, found %d.",
atmos.Nspace, (int)nz);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Read data --- */
if (( pop_var = H5Dopen2(ncid, POP_NAME, H5P_DEFAULT)) < 0)
HERR(routineName);
dims[0] = molecule->Nv;
dims[1] = atmos.Nspace;
if (( mem_dspace = H5Screate_simple(2, dims, NULL) ) < 0) HERR(routineName);
/* File dataspace */
offset[0] = 0;
offset[1] = mpi.ix;
offset[2] = mpi.iy;
offset[3] = mpi.zcut;
count[0] = molecule->Nv;
count[3] = atmos.Nspace;
if (( file_dspace = H5Dget_space(pop_var) ) < 0) HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dread(pop_var, H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, molecule->nv[0]) ) < 0) HERR(routineName);
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (( H5Dclose(pop_var) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------------- readPopulations_p.c -- */
void readPopulations(Atom *atom) {
/* --- Read populations from file.
Note: readPopulations only reads the true populations and not
the LTE populations.
Note2: This routine will not work yet in HFD5. Access to the aux file
needs to be better regulated in OLD_POPULATIONS cases (ie, append
and read/write acess). The code below assumes the file is already
open, which may not be the case.
-- -------------- */
const char routineName[] = "readPopulations_p";
char group_name[ARR_STRLEN], *atmosID;
int nz, nlevel;
H5T_class_t type_class;
size_t attr_size;
hsize_t offset[] = {0, 0, 0, 0};
hsize_t count[] = {1, 1, 1, 1};
hsize_t dims[4];
hid_t ncid, file_dspace, mem_dspace, pop_var;
/* --- Open atom group --- */
sprintf(group_name,(atom->ID[1] == ' ') ? "atom_%.1s" : "atom_%.2s", atom->ID);
if (( ncid = H5Gopen(io.aux_ncid, group_name, H5P_DEFAULT) ) < 0)
HERR(routineName);
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(io.aux_ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(io.aux_ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid, ".", "nlevel", &nlevel) ) < 0)
HERR(routineName);
if (nlevel != atom->Nlevel) {
sprintf(messageStr,
"Number of levels mismatch: expected %d, found %d.",
atom->Nlevel, (int)nlevel);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(io.aux_ncid, ".", "nz", &nz) ) < 0)
HERR(routineName);
if (nz < atmos.Nspace) {
sprintf(messageStr,
"Number of depth points mismatch: expected %ld, found %d.",
atmos.Nspace, (int)nz);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Read data --- */
if (( pop_var = H5Dopen2(ncid, POP_NAME, H5P_DEFAULT)) < 0)
HERR(routineName);
dims[0] = atom->Nlevel;
dims[1] = atmos.Nspace;
if (( mem_dspace = H5Screate_simple(2, dims, NULL) ) < 0) HERR(routineName);
/* File dataspace */
offset[0] = 0;
offset[1] = mpi.ix;
offset[2] = mpi.iy;
offset[3] = mpi.zcut;
count[0] = atom->Nlevel;
count[3] = atmos.Nspace;
if (( file_dspace = H5Dget_space(pop_var) ) < 0) HERR(routineName);
if (( H5Sselect_hyperslab(file_dspace, H5S_SELECT_SET, offset,
NULL, count, NULL) ) < 0) HERR(routineName);
if (( H5Dread(pop_var, H5T_NATIVE_DOUBLE, mem_dspace,
file_dspace, H5P_DEFAULT, atom->n[0]) ) < 0) HERR(routineName);
if (( H5Sclose(mem_dspace) ) < 0) HERR(routineName);
if (( H5Sclose(file_dspace) ) < 0) HERR(routineName);
if (( H5Dclose(pop_var) ) < 0) HERR(routineName);
return;
}
/* ------- begin -------------------- init_aux_existing.c --- */
void init_aux_existing(void) {
const char routineName[] = "init_aux_existing";
int i, nlevel, nline, ncont;
size_t attr_size;
hid_t ncid, ncid_atom, ncid_mol, plist;
H5T_class_t type_class;
char group_name[ARR_STRLEN], *atmosID;
Atom *atom;
Molecule *molecule;
/* Open the file with parallel MPI-IO access */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fopen(AUX_FILE, H5F_ACC_RDWR, plist) ) < 0)
HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
io.aux_ncid = ncid;
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Create arrays for multiple-atom/molecule output */
io.aux_atom_ncid = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_ncid = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
if (input.p15d_wpop) {
io.aux_atom_pop = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_poplte = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_mol_pop = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
io.aux_mol_poplte = (hid_t *) malloc(atmos.Nactivemol * sizeof(hid_t));
}
if (input.p15d_wrates) {
io.aux_atom_RijL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiL = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RijC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
io.aux_atom_RjiC = (hid_t *) malloc(atmos.Nactiveatom * sizeof(hid_t));
}
/* --- Group loop over active ATOMS --- */
for (i=0; i < atmos.Nactiveatom; i++) {
atom = atmos.activeatoms[i];
/* --- Get ncid of the atom group --- */
sprintf(group_name,(atom->ID[1] == ' ') ? "atom_%.1s" : "atom_%.2s", atom->ID);
if (( io.aux_atom_ncid[i] = H5Gopen(io.aux_ncid, group_name,
H5P_DEFAULT) ) < 0) HERR(routineName);
ncid_atom = io.aux_atom_ncid[i];
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid_atom, ".", "nlevel", &nlevel) ) < 0)
HERR(routineName);
if (nlevel != atom->Nlevel) {
sprintf(messageStr,
"Number of levels mismatch: expected %d, found %d.",
atom->Nlevel, (int)nlevel);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid_atom, ".", "nline", &nline) ) < 0)
HERR(routineName);
if (nline != atom->Nline) {
sprintf(messageStr,
"Number of lines mismatch: expected %d, found %d.",
atom->Nline, (int)nline);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid_atom, ".", "ncontinuum", &ncont) ) < 0)
HERR(routineName);
if (ncont != atom->Ncont) {
sprintf(messageStr,
"Number of continua mismatch: expected %d, found %d.",
atom->Ncont, (int)ncont);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Open datasets collectively ---*/
if (input.p15d_wpop) {
if (( io.aux_atom_pop[i] = H5Dopen(ncid_atom, POP_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.aux_atom_poplte[i] = H5Dopen(ncid_atom, POPLTE_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
}
if (input.p15d_wrates) {
if (( io.aux_atom_RijL[i] = H5Dopen(ncid_atom, RIJ_L_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.aux_atom_RjiL[i] = H5Dopen(ncid_atom, RJI_L_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (atom->Ncont > 0) {
if (( io.aux_atom_RijC[i] = H5Dopen(ncid_atom, RIJ_C_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.aux_atom_RjiC[i] = H5Dopen(ncid_atom, RJI_C_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
}
}
} /* end active ATOMS loop */
/* --- Group loop over active MOLECULES --- */
for (i=0; i < atmos.Nactivemol; i++) {
molecule = atmos.activemols[i];
/* --- Get ncid of the molecule group --- */
sprintf( group_name, "molecule_%s", molecule->ID);
if (( io.aux_mol_ncid[i] = H5Gopen(io.aux_ncid, group_name,
H5P_DEFAULT) ) < 0) HERR(routineName);
ncid_mol = io.aux_mol_ncid[i];
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid_mol, ".", "nlevel_vibr", &nlevel) ) < 0)
HERR(routineName);
if (nlevel != molecule->Nv) {
sprintf(messageStr,
"Number of levels mismatch: expected %d, found %d.",
molecule->Nv, (int)nlevel);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid_mol, ".", "nline_molecule", &nline) ) < 0)
HERR(routineName);
if (nline != molecule->Nrt) {
sprintf(messageStr,
"Number of lines mismatch: expected %d, found %d.",
molecule->Nrt, (int)nline);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid_mol, ".", "nJ", &ncont) ) < 0)
HERR(routineName);
if (ncont != molecule->NJ) {
sprintf(messageStr,
"Number of J mismatch: expected %d, found %d.",
molecule->NJ, (int)ncont);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Open datasets collectively ---*/
if (input.p15d_wpop) {
if (( io.aux_mol_pop[i] = H5Dopen(ncid_mol, POP_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
if (( io.aux_mol_poplte[i] = H5Dopen(ncid_mol, POPLTE_NAME,
H5P_DEFAULT) ) < 0) HERR(routineName);
}
} /* end active MOLECULES loop */
return;
}
static herr_t make_attributes( hid_t loc_id, const char* obj_name )
{
int rank_out;
hsize_t *dims_out = 0;
H5T_class_t type_class;
size_t type_size;
int i;
char attr_str_in[] = {"My attribute"};
char attr_str_out[20];
char attr_char_in[5] = {1,2,3,4,5};
char attr_char_out[5];
short attr_short_in[5] = {1,2,3,4,5};
short attr_short_out[5];
int attr_int_in[5] = {1,2,3,4,5};
int attr_int_out[5];
long attr_long_in[5] = {1,2,3,4,5};
long attr_long_out[5];
float attr_float_in[5] = {1,2,3,4,5};
float attr_float_out[5];
double attr_double_in[5] = {1,2,3,4,5};
double attr_double_out[5];
unsigned char attr_uchar_in[5] = {1,2,3,4,5};
unsigned char attr_uchar_out[5];
unsigned short attr_ushort_in[5] = {1,2,3,4,5};
unsigned short attr_ushort_out[5];
unsigned int attr_uint_in[5] = {1,2,3,4,5};
unsigned int attr_uint_out[5];
unsigned long attr_ulong_in[5] = {1,2,3,4,5};
unsigned long attr_ulong_out[5];
/*-------------------------------------------------------------------------
* H5LTset_attribute_string test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_string");
/* Set the attribute */
if ( H5LTset_attribute_string( loc_id, obj_name, ATTR1_NAME, attr_str_in ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_string test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_string");
/* Get the attribute */
if ( H5LTget_attribute_string( loc_id, obj_name, ATTR1_NAME, attr_str_out ) < 0 )
return -1;
if ( strcmp( attr_str_in, attr_str_out ) != 0 )
{
return -1;
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_char test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_char");
/* Set the attribute */
if ( H5LTset_attribute_char( loc_id, obj_name, ATTR2_NAME, attr_char_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_char test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_char");
/* Get the attribute */
if ( H5LTget_attribute_char( loc_id, obj_name, ATTR2_NAME, attr_char_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_char_in[i] != attr_char_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR2_NAME, H5T_NATIVE_CHAR, attr_char_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_char_in[i] != attr_char_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_short test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_short");
/* Set the attribute */
if ( H5LTset_attribute_short( loc_id, obj_name, ATTR3_NAME, attr_short_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_short test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_short");
/* Get the attribute */
if ( H5LTget_attribute_short( loc_id, obj_name, ATTR3_NAME, attr_short_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_short_in[i] != attr_short_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR3_NAME, H5T_NATIVE_SHORT, attr_short_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_short_in[i] != attr_short_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_int");
/* Set the attribute */
if ( H5LTset_attribute_int( loc_id, obj_name, ATTR4_NAME, attr_int_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_int");
/* Get the attribute */
if ( H5LTget_attribute_int( loc_id, obj_name, ATTR4_NAME, attr_int_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_int_in[i] != attr_int_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR4_NAME, H5T_NATIVE_INT, attr_int_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_int_in[i] != attr_int_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_long");
/* Set the attribute */
if ( H5LTset_attribute_long( loc_id, obj_name, ATTR5_NAME, attr_long_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_long");
/* Get the attribute */
if ( H5LTget_attribute_long( loc_id, obj_name, ATTR5_NAME, attr_long_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_long_in[i] != attr_long_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR5_NAME, H5T_NATIVE_LONG, attr_long_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_long_in[i] != attr_long_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_uchar test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_uchar");
/* Set the attribute */
if ( H5LTset_attribute_uchar( loc_id, obj_name, ATTR6_NAME, attr_uchar_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_uchar test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_uchar");
/* Get the attribute */
if ( H5LTget_attribute_uchar( loc_id, obj_name, ATTR6_NAME, attr_uchar_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uchar_in[i] != attr_uchar_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR6_NAME, H5T_NATIVE_UCHAR, attr_uchar_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uchar_in[i] != attr_uchar_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_ushort test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_ushort");
/* Set the attribute */
if ( H5LTset_attribute_ushort( loc_id, obj_name, ATTR7_NAME, attr_ushort_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_ushort test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ushort");
/* Get the attribute */
if ( H5LTget_attribute_ushort( loc_id, obj_name, ATTR7_NAME, attr_ushort_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ushort_in[i] != attr_ushort_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR7_NAME, H5T_NATIVE_USHORT, attr_ushort_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ushort_in[i] != attr_ushort_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_uint");
/* Set the attribute */
if ( H5LTset_attribute_uint( loc_id, obj_name, ATTR8_NAME, attr_uint_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_uint");
/* Get the attribute */
if ( H5LTget_attribute_uint( loc_id, obj_name, ATTR8_NAME, attr_uint_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uint_in[i] != attr_uint_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR8_NAME, H5T_NATIVE_UINT, attr_uint_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uint_in[i] != attr_uint_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_ulong test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_ulong");
/* Set the attribute */
if ( H5LTset_attribute_ulong( loc_id, obj_name, ATTR9_NAME, attr_ulong_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ulong");
/* Get the attribute */
if ( H5LTget_attribute_ulong( loc_id, obj_name, ATTR9_NAME, attr_ulong_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ulong_in[i] != attr_ulong_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR9_NAME, H5T_NATIVE_ULONG, attr_ulong_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ulong_in[i] != attr_ulong_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_float test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_float");
/* Set the attribute */
if ( H5LTset_attribute_float( loc_id, obj_name, ATTR10_NAME, attr_float_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_float test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_float");
/* Get the attribute */
if ( H5LTget_attribute_float( loc_id, obj_name, ATTR10_NAME, attr_float_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_float_in[i] != attr_float_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR10_NAME, H5T_NATIVE_FLOAT, attr_float_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_float_in[i] != attr_float_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_double test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_double");
/* Set the attribute */
if ( H5LTset_attribute_double( loc_id, obj_name, ATTR11_NAME, attr_double_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_double test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_double");
/* Get the attribute */
if ( H5LTget_attribute_double( loc_id, obj_name, ATTR11_NAME, attr_double_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_double_in[i] != attr_double_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR11_NAME, H5T_NATIVE_DOUBLE, attr_double_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_double_in[i] != attr_double_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_ndims test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ndims");
if ( H5LTget_attribute_ndims( loc_id, obj_name, ATTR2_NAME, &rank_out ) < 0 )
return -1;
if ( rank_out != 1 ) {
return -1;
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_info test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_info");
dims_out = (hsize_t*) malloc( sizeof(hsize_t) * rank_out );
if ( H5LTget_attribute_info( loc_id, obj_name, ATTR2_NAME, dims_out, &type_class,
&type_size) < 0 )
return -1;
for (i = 0; i < rank_out; i++)
{
if ( dims_out[i] != 5 ) {
return -1;
}
}
if ( type_class != H5T_INTEGER ) {
return -1;
}
if ( dims_out )
free( dims_out );
PASSED();
return 0;
}
asynStatus hdf5Driver::openFile (const char *path)
{
asynStatus status = asynSuccess;
const char *functionName = "loadFile";
hid_t fileId, groupId;
H5G_info_t groupInfo;
size_t totalFrames = 0;
size_t maxWidth = 0, maxHeight = 0;
// Reset some parameters
setIntegerParam(HDF5DatasetsCount, 0);
setIntegerParam(HDF5TotalFrames, 0);
setIntegerParam(HDF5FirstFrame, 0);
setIntegerParam(HDF5LastFrame, 0);
setIntegerParam(HDF5CurrentFrame, 0);
setIntegerParam(ADMaxSizeX, 0);
setIntegerParam(ADMaxSizeY, 0);
callParamCallbacks();
// Get a file handle
if((fileId = H5Fopen(path, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
{
asynPrint(pasynUserSelf, ASYN_TRACE_ERROR,
"%s:%s couldn't open file '%s'\n",
driverName, functionName, path);
status = asynError;
goto end;
}
// Get a handle to the '/entry' group
if((groupId = H5Gopen2(fileId, "/entry", H5P_DEFAULT)) < 0)
{
asynPrint(pasynUserSelf, ASYN_TRACE_ERROR,
"%s:%s couldn't open 'entry' group\n",
driverName, functionName);
status = asynError;
goto closeFile;
}
// Need groupInfo to obtain number of links
if(H5Gget_info(groupId, &groupInfo))
{
asynPrint(pasynUserSelf, ASYN_TRACE_ERROR,
"%s:%s couldn't get group info\n",
driverName, functionName);
status = asynError;
goto closeGroup;
}
// Deallocate information of previous file
if(mpDatasets)
{
for(size_t i = 0; i < mDatasetsCount; ++i)
H5Dclose(mpDatasets[i].id);
free(mpDatasets);
}
// Allocate memory to store dataset information
mpDatasets = (struct dsetInfo*) calloc(groupInfo.nlinks,
sizeof(*mpDatasets));
mDatasetsCount = 0;
// Iterate over '/entry' objects
for(size_t i = 0; i < groupInfo.nlinks; ++i)
{
// Get object name
char dsetName[256];
H5Lget_name_by_idx(groupId, ".", H5_INDEX_NAME, H5_ITER_INC, i,
dsetName, sizeof(dsetName), H5P_DEFAULT);
// If it doesn't start with 'data' it isn't a dataset. Ignore it.
if(strncmp(dsetName, "data", 4))
continue;
// Get a handle to the dataset info structure
struct dsetInfo *pDSet = &mpDatasets[mDatasetsCount++];
pDSet->id = H5Dopen2(groupId, dsetName, H5P_DEFAULT);
// Read dataset attributes
H5LTget_attribute_int(pDSet->id, ".", "image_nr_low",
&pDSet->imageNrLow);
H5LTget_attribute_int(pDSet->id, ".", "image_nr_high",
&pDSet->imageNrHigh);
// Read dimensions (assume a 3D dataset)
hsize_t dims[3] = {0,0,0};
H5LTget_dataset_info(pDSet->id, ".", dims, NULL, NULL);
totalFrames += dims[0];
pDSet->height = dims[1];
pDSet->width = dims[2];
// Calculate maxHeight and maxWidth
if(dims[1] > maxHeight)
maxHeight = dims[1];
if(dims[2] > maxWidth)
maxWidth = dims[2];
// Read type
if(parseType(pDSet->id, &pDSet->type))
{
asynPrint(pasynUserSelf, ASYN_TRACE_ERROR,
"%s:%s couldn't parse dataset type\n",
driverName, functionName);
status = asynError;
}
}
// Update parameters
setIntegerParam(HDF5DatasetsCount, (int) mDatasetsCount);
setIntegerParam(HDF5TotalFrames, (int) totalFrames);
if(mDatasetsCount > 0)
{
int firstFrame = mpDatasets[0].imageNrLow;
int lastFrame = mpDatasets[mDatasetsCount-1].imageNrHigh;
setIntegerParam(HDF5FirstFrame, firstFrame);
setIntegerParam(HDF5LastFrame, lastFrame);
setIntegerParam(HDF5CurrentFrame, firstFrame);
setIntegerParam(ADMaxSizeX, maxWidth);
setIntegerParam(ADMaxSizeY, maxHeight);
int autoLoad;
getIntegerParam(HDF5AutoLoadFrame, &autoLoad);
if(autoLoad)
{
setIntegerParam(ADImageMode, ADImageSingle);
setIntegerParam(ADNumImages, 1);
setIntegerParam(ADAcquire, 1);
epicsEventSignal(mStartEventId);
}
}
callParamCallbacks();
closeGroup:
H5Gclose(groupId);
closeFile:
H5Fclose(fileId);
end:
return status;
}
void rdiff(const char *name, hid_t f1, hid_t f2) {
hid_t g1 = H5Gopen(f1, name, H5P_DEFAULT);
hid_t g2 = H5Gopen(f2, name, H5P_DEFAULT);
if (g1 >= 0 && g2 >= 0) {
int n1 = H5Aget_num_attrs(g1);
for (int i = 0; i < n1; i++) {
char aname[MAXNAME];
hid_t a1 = H5Aopen_idx(g1, i);
assert(H5Aget_name(a1, MAXNAME, aname) < MAXNAME);
H5Aclose(a1);
if (!H5LTfind_attribute(g2, aname)) {
printf("Only in %s[%s%s]\n", file1, name, aname);
continue;
}
int d1, d2;
H5LTget_attribute_ndims(f1, name, aname, &d1);
H5LTget_attribute_ndims(f2, name, aname, &d2);
assert(d1 <= 1 && d2 <= 1);
hsize_t dims1, dims2;
H5T_class_t t1, t2;
size_t ts1, ts2;
H5LTget_attribute_info(f1, name, aname, &dims1, &t1, &ts1);
H5LTget_attribute_info(f2, name, aname, &dims2, &t2, &ts2);
assert(t1 == t2);
assert(t1 == H5T_INTEGER || t1 == H5T_FLOAT || t1 == H5T_STRING);
if (t1 == H5T_INTEGER) {
assert(d1==0 || (dims1 == 1 && dims2 == 1));
assert(ts1 == 4 && ts2 == 4);
int v1, v2;
H5LTget_attribute_int(f1, name, aname, &v1);
H5LTget_attribute_int(f2, name, aname, &v2);
if (v1 != v2) {
printf("%s[%s%s]=%d %s[%s%s]=%d\n", file1, name, aname, v1, file2, name, aname, v2);
}
}
if (t1 == H5T_FLOAT) {
assert(d1==0 || (dims1 == 1 && dims2 == 1));
assert(ts1 == 4 && ts2 == 4);
float v1, v2;
H5LTget_attribute_float(f1, name, aname, &v1);
H5LTget_attribute_float(f2, name, aname, &v2);
if (v1 != v2) {
printf("%s[%s%s]=%g %s[%s%s]=%g\n", file1, name, aname, v1, file2, name, aname, v2);
}
}
if (t1 == H5T_STRING) {
assert(ts1 < 256 && ts2 < 256);
char buf1[256];
char buf2[256];
H5LTget_attribute_string(f1, name, aname, buf1);
H5LTget_attribute_string(f2, name, aname, buf2);
if (strcmp(buf1, buf2)) {
printf("%s[%s%s]=%s %s[%s%s]=%s\n", file1, name, aname, buf1, file2, name, aname, buf2);
}
}
}
int n2 = H5Aget_num_attrs(g2);
for (int i = 0; i < n2; i++) {
char aname[MAXNAME];
hid_t a2 = H5Aopen_idx(g2, i);
assert(H5Aget_name(a2, MAXNAME, aname) < MAXNAME);
H5Aclose(a2);
if (!H5LTfind_attribute(g1, aname)) {
printf("Only in %s[%s%s]\n", file2, name, aname);
continue;
}
}
hsize_t nobj;
H5Gget_num_objs(g1, &nobj);
for (int i = 0; i < nobj; i++) {
char oname[MAXNAME];
assert(H5Gget_objname_by_idx(g1, i, oname, MAXNAME) < MAXNAME);
int otype = H5Gget_objtype_by_idx(g1, i);
assert(otype == H5G_DATASET);
if (!H5LTfind_dataset(g2, oname)) {
printf("Only in %s[%s%s]\n", file1, name, oname);
continue;
}
hsize_t dims1[2], dims2[2];
H5T_class_t t1, t2;
size_t ts1, ts2;
H5LTget_dataset_info(g1, oname, dims1, &t1, &ts1);
H5LTget_dataset_info(g2, oname, dims2, &t2, &ts2);
if (dims1[0] != dims2[0] || dims1[1] != dims2[1]) {
printf("%s[%s%s](%d,%d) != %s[%s%s](%d,%d)\n",
file1, name, oname, dims1[1], dims1[0],
file2, name, oname, dims2[1], dims2[0]);
continue;
}
float *data1 = malloc(dims1[0]*dims1[1]*sizeof(float));
float *data2 = malloc(dims1[0]*dims1[1]*sizeof(float));
H5LTread_dataset_float(g1, oname, data1);
H5LTread_dataset_float(g2, oname, data2);
float maxdiff = 0;
for (int i = dims1[0]*dims1[1]-1; i >= 0; i--) {
float d = data1[i] - data2[i];
if (d < 0) d = -d;
if (d > maxdiff) maxdiff = d;
}
printf("max |%s[%s%s] - %s[%s%s]| = %g\n",
file1, name, oname, file2, name, oname, maxdiff);
free(data1); free(data2);
}
H5Gget_num_objs(g2, &nobj);
for (int i = 0; i < nobj; i++) {
char oname[MAXNAME];
assert(H5Gget_objname_by_idx(g2, i, oname, MAXNAME) < MAXNAME);
int otype = H5Gget_objtype_by_idx(g2, i);
assert(otype == H5G_DATASET);
if (!H5LTfind_dataset(g1, oname)) {
printf("Only in %s[%s%s]\n", file2, name, oname);
continue;
}
}
H5Gclose(g1);
H5Gclose(g2);
} else if (g1 >= 0) {
printf("Only in %s:%s\n", file1, name);
H5Gclose(g1);
} else if (g2 >= 0) {
printf("Only in %s:%s\n", file2, name);
H5Gclose(g2);
} else {
printf("Group %s does not exist in either file.\n", name);
}
}
/***********************************************************************
NAME: ias_ancillary_read
PURPOSE: Calls routines to read ancillary and ephemeris data
RETURNS: Integer status code of SUCCESS or ERROR
NOTES: Calling routine is responsible for ensuring a valid filename
************************************************************************/
int ias_ancillary_read
(
const char *ancillary_filename, /* I: Name of data file */
IAS_ANC_ATTITUDE_DATA **attitude_data, /* I/O: Pointer to attitude
data */
IAS_ANC_EPHEMERIS_DATA **ephemeris_data /* I/O: Pointer to ephemeris
data */
)
{
hid_t hdf_file_id = -1; /* HDF5 file handle */
herr_t hdf_error_status = -1; /* HDF5 error status code; negative
values indicate an error */
int file_format_version = 0; /* File format version */
int rank = 0; /* Number of dimensions for the
format version attribute */
H5T_class_t type_class; /* Type class identifier */
size_t type_size = 0; /* Size of datatype in bytes */
hsize_t version_dims = 0; /* Format version array dimension */
IAS_ANC_ATTITUDE_DATA *attitude_read = NULL;
/* working attitude data buffer */
IAS_ANC_EPHEMERIS_DATA *ephemeris_read = NULL;
/* working ephemeris data buffer */
/* Initialize the pointers so caller has something to check against */
*attitude_data = NULL;
*ephemeris_data = NULL;
/* Make sure the ancillary file is "valid" */
if (!ias_ancillary_is_ancillary_file(ancillary_filename))
{
IAS_LOG_ERROR("Ancillary file %s not valid", ancillary_filename);
return ERROR;
}
/* Open the file for reading. */
hdf_file_id = H5Fopen(ancillary_filename, H5F_ACC_RDONLY, H5P_DEFAULT);
if (hdf_file_id < 0)
{
IAS_LOG_ERROR("Opening ancillary data file %s", ancillary_filename);
return ERROR;
}
/* Verify the file format version attribute has a dimension of 1 */
hdf_error_status = H5LTget_attribute_ndims(hdf_file_id, "/",
FILE_FORMAT_VERSION_ATTRIBUTE_NAME, &rank);
if (hdf_error_status < 0)
{
IAS_LOG_ERROR("Retrieving file format version attribute dimensions "
"in ancillary file %s", ancillary_filename);
return ERROR;
}
if (rank != 1) /* Should only be 1D array */
{
IAS_LOG_ERROR("Invalid rank %d detected for file format version "
"attribute in ancillary file %s, should be 1",
rank, ancillary_filename);
return ERROR;
}
/* The file format version attribute should be a scalar of integer
data type*/
hdf_error_status = H5LTget_attribute_info(hdf_file_id, "/",
FILE_FORMAT_VERSION_ATTRIBUTE_NAME, &version_dims,
&type_class, &type_size);
if ((hdf_error_status < 0) || (version_dims != 1)
|| (type_class != H5T_INTEGER)
|| (type_size != sizeof(int)))
{
IAS_LOG_ERROR("Invalid file format version attribute information "
"in ancillary file %s", ancillary_filename);
return ERROR;
}
/* Read the file format version information */
hdf_error_status = H5LTget_attribute_int(hdf_file_id, "/",
FILE_FORMAT_VERSION_ATTRIBUTE_NAME, &file_format_version);
if (hdf_error_status < 0)
{
IAS_LOG_ERROR("Reading file format version attribute in ancillary "
"file %s", ancillary_filename);
H5Fclose(hdf_file_id);
return ERROR;
}
/* Read the attitude data from the file. */
attitude_read = read_attitude_data(hdf_file_id, file_format_version);
if (attitude_read == NULL)
{
IAS_LOG_ERROR("Reading attitude data from ancillary data file %s",
ancillary_filename);
H5Fclose(hdf_file_id);
return ERROR;
}
/* Read the ephemeris data from the file. */
ephemeris_read = read_ephemeris_data(hdf_file_id, file_format_version);
if (ephemeris_read == NULL)
{
IAS_LOG_ERROR("Reading ephemeris data from ancillary data file %s",
ancillary_filename);
ias_ancillary_free_attitude(attitude_read);
H5Fclose(hdf_file_id);
return ERROR;
}
/* Close the file now that the attitude and ephemeris data have been
read from it. */
hdf_error_status = H5Fclose(hdf_file_id);
if (hdf_error_status < 0)
{
IAS_LOG_ERROR("Closing ancillary data file %s", ancillary_filename);
ias_ancillary_free_attitude(attitude_read);
ias_ancillary_free_ephemeris(ephemeris_read);
return ERROR;
}
/* Point the input pointers to the working buffers. */
*attitude_data = attitude_read;
*ephemeris_data = ephemeris_read;
/* Done */
return SUCCESS;
}
int SpIO_FreadModel(const SpFile *sfp, const SpFile *popsfp, SpModel *model, int *read_pops)
{
int status = 0;
Deb_ASSERT(model->parms.mol == NULL);
Deb_ASSERT(model->grid == NULL);
#if 1
/* pre-check format version */
if(!status){
const char *default_format = "SPARX format v3";
char *format = NULL;
status = SpIO_H5GetAttribute_string(sfp->h5f_id, "/", "format", &format);
if(strncmp(format, default_format, strlen("SPARX format v3"))){
printf("The format is not '%s' (%s)\n", default_format, format);
status = 1;
}
free(format);
}
#endif
/* Read coordinate name */
if(!status){
char *coordinate = NULL;
status = SpIO_H5GetAttribute_string(sfp->h5f_id, "/", "geom", &coordinate);
/* Load molecule if present */
if(strlen(coordinate) > 0) {
DatINode *geom = Dat_IList_NameLookup(GEOM_TYPES, coordinate);
model->parms.geom = geom->idx;
}
free(coordinate);
}
herr_t hstatus;
/* Read T_cmb */
if(!status) {
hstatus = H5LTget_attribute_double(sfp->h5f_id, "/", "T_cmb", &model->parms.T_cmb);
if(hstatus < 0)
status = 1;
}
/* Read T_in */
if(!status) {
hstatus = H5LTget_attribute_double(sfp->h5f_id, "/", "T_in", &model->parms.T_in);
if(hstatus < 0)
status = 1;
}
/* Read molecule name */
if(!status){
char *mol_name = NULL;
status = SpIO_H5GetAttribute_string(sfp->h5f_id, "/", "molec", &mol_name);
/* Load molecule if present */
if(strlen(mol_name) > 0) {
if(!(model->parms.mol = SpIO_FreadMolec(mol_name)))
status = 1;
}
free(mol_name);
}
/* Read pops-switch */
if(!status) {
hstatus = H5LTget_attribute_int(sfp->h5f_id, "/", "pops", &model->parms.pops);
if(hstatus < 0)
status = 1;
}
/* Read dust-switch */
if(!status) {
hstatus = H5LTget_attribute_int(sfp->h5f_id, "/", "dust", &model->parms.dust);
if(hstatus < 0)
status = 1;
}
/* Read polariz-switch */
if(!status) {
hstatus = H5LTget_attribute_int(sfp->h5f_id, "/", "polariz", &model->parms.polariz);
if(hstatus < 0)
status = 1;
}
/* Read z (zeeman splitting) factor */
if(!status) {
hstatus = H5LTget_attribute_int(sfp->h5f_id, "/", "z", &model->parms.z);
if(hstatus < 0)
status = 1;
}
#if 0
/* Set velocity field: the "velfield" attribute is expected
* to contain a Python function named "Vgas((x1,x2,x3),(min1,min2,min3),(max1,max2,max3)" where
* (x1,x2,x3) are the three coordinates of the ray position, (min1,min2,min3) are the lower
* bounds of the bounding box, and (max1,max2,max3) are the upper baounds of the bounding
* box. An example Vgas function would be:
* def Vgas((x1, x2, x3), (min1, min2, min3), (max1, max2, max3)):"
* return [0,0,0]"
*/
if(!status) {
char *velfield = NULL;
//if(!strncmp(velfield, "grid", strlen(velfield))) {
if(!strncmp(velfield, "grid", strlen("grid"))) {
model->parms.velfield = NULL;
}
else {
status = PyRun_SimpleString(velfield);
PyObject *__main__ = NULL, *ret = NULL;
__main__ = PyImport_AddModule("__main__");
model->parms.velfield = PyObject_GetAttrString(__main__, "Vgas");
Py_INCREF(model->parms.velfield);
/* Try calling the function and make sure it returns a sequence of length 3 */
char format[] = "(d,d,d),(d,d,d),(d,d,d)";
ret = PyObject_CallFunction(model->parms.velfield, format, 0, 0, 0, 0, 0, 0, 0, 0, 0);
if(!PySequence_Check(ret)) {
PyWrErr_SetString(PyExc_Exception, "Vgas() does not return a vector!");
status = 1;
}
}
free(velfield);
}
#endif
/* Load grid */
if(!status)
status =
SpIO_H5ReadGrid(
sfp->h5f_id,
(*read_pops) ? popsfp->h5f_id : NULL,
&model->grid,
&model->parms,
read_pops
);
/* Cleanup */
if(status)
PyWrErr_SetString(PyExc_Exception, "Error reading model from file `%s'", sfp->name);
return status;
}
